The Captain and the Doctor
by atagal8907
Summary: Jane Rizzoli is the captain of the U.S.S. Salvation. Captain Rizzoli and her crew are about to embark on one year mission in the Delta Quadrant. But before they can embark on this mission the Salvation is in need of a new Chief Medical Officer.
1. Chapter 1

**Title:** The Captain and the Doctor

**Disclaimer:** All "Rizzoli & Isles" characters are property of Tess Gerritsen and TNT. All "Star Trek" characters are property of Gene Rodenberry and Paramount Picture.

**Rating:** T

**Pairing:** Jane Rizzoli / Maura Isles (eventually)

**Summary:** Jane Rizzoli is the captain of the U.S.S. Salvation. Captain Rizzoli and her crew are about to embark on one year mission in the Delta Quadrant. But before they can embark on this mission the Salvation is in need of a new Chief Medical Officer.

**A/N:** This is an A/U story. Taking the Rizzoli & Isles universe and putting it into the Star Trek universe. This story is not beta'd so any mistakes are my own. If any readers find any mistakes or have any suggestions please let me know. Also, please note that this story will eventually be about a romantic relationship between two women. If this offends any readers please do not read.

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**Chapter One**

July 26, 2431

The windows of the Starfleet Headquarters shimmered in the early morning sun as Jane quickly climbed the steps of the building. The massive doors of the building slid open, welcoming her inside.

Jane quickly made her towards the stairs, deciding to take the stairs instead. Today Jane Rizzoli was in a good mood with a spring in her step. Jane quickly made her way up the stairs to the top floor where Vice Admiral Cavanaugh's office was located.

After ten minutes of climbing stairs Jane finally made it to the top and quickly navigated her way to the vice admiral's office. Jane slowly walked up to the desk in the hallway.

"Good morning Mrs. Thompson, I have meeting with Admiral Cavanaugh at 0830 hours." Jane said to the grey-hair woman sitting behind the desk.

"Good morning Captain Rizzoli, I let Admiral Cavanaugh know you're here," said the smiling Mrs. Thompson.

Jane nodded her head before walking to the large window that over saw the grounds of the headquarters.

Jane's eyes roamed the picturesque view before her. In the distance she could see the outline of the Golden Gate Bridge standing tall and proud. A sense of melancholy enveloped her, for two weeks from today she and her crew will far from home.

The voice of Mrs. Thompson pulled Jane from her own thoughts, "Captain Rizzoli, the admiral will see you now."

Taking a moment to check her appearance Jane replied, "Thank you Mrs. Thompson."

Jane slowly walked to the closed doors of Admiral Cavanaugh and waited for the doors to slide open. The doors slid open a matter of seconds and Jane stepped inside the office.

Jane sat and waited patiently as Admiral Cavanaugh finished up his current task.

Admiral Cavanaugh sat behind his desk as he entered data into his PADD. The bleeping sounds from the PADD eased the silent atmosphere of the room.

"Finally, I was thinking I wouldn't be finished with entry by 0900 hours," said a relieved Admiral Cavanaugh.

Putting the PADD on his desk he finally turned his full attention to Jane. "Good morning Captain Rizzoli, how are you doing today?"

"I'm doing well Admiral Cavanaugh, anxious to find out who my new Chief Medical Officer is," replied Jane.

Admiral Cavanaugh smiled and nodded his head before picking up another PADD on his desk, "Well, you won't have to wait any longer Captain Rizzoli. I believe I have found your new Chief Medical Officer and I have to say you are one lucky captain."

The admiral's last words confused Jane, "Lucky sir?" Jane asked.

"Lucky indeed, for your new Chief Medical Officer is none other than Dr. Maura Isles."

This confused Jane even more for she never heard of a Dr. Maura Isles, "I'm sorry, but who is Dr. Maura Isles."

Admiral Cavanaugh sported a look of surprise. He thought every Starfleet officer knew who Dr. Isles was, obviously he was wrong.

Admiral Cavanaugh began to read the PADD he picked up just moments ago and began to read from it, "Dr. Maura Isles is a renowned physician at Starfleet Medical. Many physicians at Starfleet Medical consider her the female version of Dr. Leonard McCoy. She did a two year internship at the Vulcan Science Academy after she graduated from Starfleet Academy. She spent one year on Cardassia Prime helping former Maquis and Cardassian refugees. From there Dr. Isles was promoted to Lieutenant Commander and was offered a position to instruct at the Starfleet Medical Academy, which is where she is today."

Jane's confusion immediately turned into pure interest, for it sounded that this doctor had made a name for herself. Although, there was one thing that Jane needed to know.

"Dr. Isles sounds like a very accomplished woman, but I need to ask. Has she ever served on a starship before?" Jane asked.

Admiral Cavanaugh shook his head, "No."

The admiral's answer unfortunately was not what she was hoping for. She didn't have the time to introduce and integrate a doctor that's never served on a starship.

Focusing on the man in front of her Jane replied, "Sir, you know this is going to be a problem, for me especially."

Admiral Cavanaugh sighed and nodded his head in agreement, "I know, but there's no one else Captain Rizzoli. You're just going to have to do the best you can."

Jane sighed in frustration knowing that it was too late to find another medical candidate to fill the position. All that Jane could do was concede with the Admiral.

Admiral Cavanaugh gave Jane apologetic smile before handing the PADD he was holding, "This PADD contains all the information you need to know about Dr. Isles."

"Thank you, sir. I'll be sure to look over all of her information," said Jane.

Admiral Cavanaugh spoke again, "I took the liberty in setting up a meeting for you to meet Dr. Isles today at 1500 hours."

"Thank you, sir. If that's it I let you get back to work." Jane replied.

"I believe that's it. You're dismissed."

* * *

It was 1200 hours when Jane stepped into her childhood home, her senses went into overdrive when she smelled the delicious smell of Italian cooking.

Her mother was at again, cooking up a storm that could feed her entire crew for two whole months.

Shaking her head and smiling Jane made her way towards the kitchen and found her mother cooking and her brother Frankie chopping vegetables.

"Well it's about time you showed up Janie. Get a knife and help your brother chop the vegetables," said Angela.

Jane rolled her eyes and walked over to where the knives were and pulled it out of its holder.

"No hello Jane or how are you Jane?" Jane said sarcastically as she walked to where her brothers were sitting.

"Watch your tone young lady and start chopping." Angela said without turning away from her current task.

Sitting with her brothers grabbed the tomatoes and started slicing and dicing them.

"I tried getting a hold of you earlier, where were you this morning?" Frankie asked.

Jane replied, "I had a meeting with Admiral Cavanaugh, he found the "perfect" candidate to fill the Chief Medical Officer position on the Salvation."

Momentarily stopping his chopping Frankie looked at his sister and asked, "Awesome. So who did he pick for the job?"

Still slicing and dicing Jane replied, "Her name is Dr. Maura Isles, a Lieutenant Commander and instructor at Starfleet Medical Academy."

Frankie sorted through his brain and came up blank on the name, "Never heard of her. What starship did she serve on?"

Jane shook her head no, "According to her file she is a quite accomplished woman, but never served on a starship since graduating from the academy. That means I have to get our new doctor adjusted to working and living on a starship."

Frankie gave his sister a sympathetic look before he continued his chopping.

"I have a meeting with Dr. Isles at 1500 hours today." Jane told her brother as she continued to slice.

Hearing this Angela butted into the conversation, "At least Janie you will have a female companion on that ship. Maybe she can help catch a man on that ship or whatever planet you visit. Maybe a nice Vulcan or perhaps a Betazoid."

Angela's comment made Frankie laugh at his mother's never ending need to get Jane to find a guy no matter what species they are.

Jane shook her head and smiled before letting out a small laugh, "Whatever you say Ma."

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**A/N:** As some readers may know that I had this story up quite some time, but I took the story down to revamp it. I apologize to the readers that previously took the time to read and review this story before for the unexpected deletion of the story. Reviews are always appreciated, but please be sure to keep them respectful.


	2. Chapter 2

***For the full story summary and story details, please refer to Chapter One of the story.*  
**

**Title: **The Captain and the Doctor

**Disclaimer: **All "Rizzoli & Isles" characters are the property of Tess Gerritsen and TNT. All "Star Trek" characters are the property of Gene Roddenberry and Paramount Picture.

**A/N: **To the readers and reviewers I want to say thank you for giving this fanfic story a chance. This story is beta'd so any mistakes are my own. Unfortunately, I am still unable to find a beta reader for my story. **So if any readers out there are interested or possibly suggest a beta reader, please send a PM on my fanfiction account.** If any readers find any mistakes or have any suggestions please let me know via review or PM.

* * *

**Chapter Two  
**

July 26, 2431 (later the same day)

Dr. Maura Isles let out a heavy sigh as she made her way towards her office.

Today was particularly a trying day due to the fact that her former fiancé Garrett Fairfield was calling her non-stop.

"What did I ever see in that lying, cheating, and poor excuse for a man?" Maura said to herself.

"_You loved him that's why_," said Maura's conscience.

Shaking her head Maura continued her path towards her office. She passed by a few of her colleagues that greeted her as they passed by. Maura returned the gesture with a smile and a small nod.

At that moment she noticed her assistant speaking amenable to a female Starfleet officer. Actually, the assistant look more like she was downright flirting with the female officer.

"Holly, what I am going to do with you?" Maura said, startling the assistant.

"Dr. Isles, I was just making friendly conversation with um…what's your name?"

The female officer let out a relieved breath at the doctor's excellent timing the female officer responded, "I am Captain Jane Rizzoli and I am here to meet with you Dr. Isles."

Remembering her communication with Admiral Cavanaugh about the meeting with Captain Rizzoli, Maura held out her hand to the female captain.

"Of course, it is nice to meet you Captain Rizzoli. I apologize if I had kept you waiting," said Maura.

Jane grasped the offered hand and gave it a firm, yet gentle shake, "Likewise, Dr. Isles and there is no need to apologize. I am a few minutes early for our meeting."

Maura glanced at the chronometer on the wall and saw that the captain was in fact ten minutes early. Turning her attention back to Jane, Maura released her hand from the other woman's hand.

"So it would seem. If it is alright with you Captain Rizzoli, I think we should get this meeting started." Maura asked.

Jane gave Maura smile and nodded her head, "Lead the way Dr. Isles."

Smiling Maura glanced at her assistant and said, "I hope we do not have to have the same conversation again about proper conduct in the workplace."

Still embarrassed Holly shook her head in a "no" gesture as her answer to her boss.

"Good, now that we have an understanding I need for you to get something important done. Please contact Dr. Vanessa Carver, Dr. Lazio Khan, and Dr. Leon Scott and have them send their findings from the Gadara case."

"Yes, Dr. Isles. I'll get that done right away," responded Holly.

Satisfied, Maura turned to Jane and gestured her to follow. Jane followed the doctor down a small corridor to a door at the end of the hall. She watched as the doctor tapped at the control panel, thus unlocking the door. The door slid open revealing a small yet cluttered office.

Embarrassment fell upon Maura. She had completely forgotten the messy state she left her office. Through her peripheral vision Maura saw that the captain was sporting an amused look.

"I apologize for the mess Captain Rizzoli; I have been in the process of moving to my new home that I have not had the time to transport all of my work over there."

Jane turned her attention away from the cluttered office and focused her attention on the doctor. "No need to apologize Dr. Isles, my ready room too has seen it fair share of clutter."

Maura still felt a hint of embarrassment, but quickly shook it off. Gesturing for Jane to take a seat, she walked behind her desk and sat down.

Jane sat in the chair in front of the large desk and took out a couple of PADDs from the small black case.

"If you're ready then let us begin."

"I am sure that Admiral Cavanaugh has already informed you about what this meeting entails." Jane stated.

"Yes, Admiral Cavanaugh has informed that you are in need of a Chief Medical Officer aboard your starship, the U.S.S. Salvation," replied Maura.

Jane continued, "That is correct and the admiral was very adamant that you are the right person for the job."

"I see. Well, I do not why he would choose me out of all the other qualified officers and doctors to take this place on you starship?" replied Maura.

Nodding Jane responded, "Me too, but there are reasons for it and I hope that the both of us can figure it."

"Agreed," Said Maura, "I feel the best way to approach this particular situation is for you to ask me questions."

Jane nodded her head in agreement before turning her attention to the PADD in her hand. "I was looking over the information that Admiral Cavanaugh provided and I am quite impressed with your personal record."

"Thank you." Maura replied.

"I am curious though, I notice that there is no record of you serving on a starship since graduating from Starfleet Academy and Starfleet Medical Academy. Would you mind answering why you were not assigned to serve on a starship?"

"Of course, after graduating from Starfleet Academy and Starfleet Medical Academy I was offered the position of Chief Medical Officer aboard the U.S.S. Bering by Captain Mesmer."

"Wow. Fresh out the academy and offered the position of Chief Medical Officer aboard the U.S.S. Bering. The Bering was tough ship to work on especially with Captain Mesmer in the Captain's seat. Still, the question I asked is why you were never assigned or accepted the position" Jane asked.

Leaning back into her chair Maura replied, "I declined Captain Mesmer's offer because an internship position at the Vulcan Science Academy was available."

Looking at the PADD, Jane scanned through the PADD looking for information on the doctor's internship on Vulcan.

"It would seem that Admiral Cavanaugh failed to give this bit of information. Would you mind telling me about your time on Vulcan and at the Vulcan Science Academy?" asked Jane.

"Living on Vulcan was hard at first because like with anyone adapting to a new environment and culture it took some time to get use to it." Maura said, with a content look on her face.

Jane nodded her head, "During your internship at the Vulcan Science Academy, who did you work with?"

"During my internship I worked with many scientists, but the most prominent scientist and mentor was Dr. Serranstivlen," replied Maura

"Ah, I have had the honor of meeting Dr. Serranstivlen during a peace conference a few months ago. He is not your typical Vulcan."

"Yes, Dr. Serranstivlen is more of a progressive Vulcan when it comes to other cultures. That is why I worked with him most of the time while on Vulcan."

Giving Maura a small smile, Jane continued on with another question, "I noticed that you are an accomplished linguist and are well versed in various species languages and their dialects."

Maura nodded her head and said, "Being a linguist is a wonderful tool especially when you are a doctor. We as physicians and healers deal with many types of species and it is always a good idea to understand our patient's needs."

"It is understandable especially with the job we have and the various cultures we've meet on our journeys." Jane replied.

"I had the same thought, it amazing how far we have come and yet there is still so much more us to explore and learn from."

Jane nodded her head. "Indeed."

Satisfied with the doctor's answers Jane continued her questioning, "I see that you also spent time on Cardassia Prime, what did you experience there?"

Maura's mood changed with the mention of Cardassia Prime to a more somber tone. Jane noticed the immediate change and became curious. "Dr. Isles, did something happen on Cardassia Prime?"

Sighing heavily Maura was hoping the topic of Cardassia Prime would be overlooked. But she knew that it was something to be discussed. Taking a deep breath she spoke in a low, but understandable voice.

"My time on Cardassia Prime was dark and sad. I was part of a relief group called Doctors for Life; we spent a year in remote parts of Cardassia Prime. We aided displaced Cardassian refugees, former Maquis and Bajoran prisoners. We were their primary source for medical attention during reconstruction of Cardassia Prime."

Seeing and hearing the sadness in the doctor's words, Jane was about to tell the doctor that she did not have say anything else. Before she was able to say thing anything, the doctor's voice stopped her.

"It was our tenth month in a remote part of Cardassia Prime and the relief group I was with was aiding a small refugee camp in need of medical help. The small group were attacked by a guerilla war party of former soldiers of the old Cardassian Empire. The war party executed most of the refugees for treason and desertion, many of the women and children taken to serve as slaves for this war party."

Hearing this Jane could not help the disgusting taste that developed in her mouth. It made Jane sick and sad that there were people on Cardassia Prime still struggling from the aftermath of the Reformation War of 2426.

"It was late one evening when guerilla soldiers attacked our base camp and um …" at this moment Maura let out a shaky breath as images of that night assaulted her mind.

Seeing the distress the woman was in Jane spoke in a calm and soothing voice, "It's alright Dr. Isles, you don't have to say anything more.

Trying to control her emotions Maura took a calm breath and said, "I'm sorry for breaking down like that in front of you Captain Rizzoli. It is embarrassing and unbecoming of a Starfleet officer."

Jane shook her head and said, "No, it is not unbecoming of a Starfleet officer nor is it embarrassing. We are beings that have the right to breakdown when the situation calls for it. Do not be ashamed of that Dr. Isles."

Sniffing Maura nodded her head in understanding before speaking, "I'll take that to heart Captain Rizzoli. So let us move away from this somber topic to lighter ones, shall we?"

Smiling Jane replied, "Agreed."

* * *

For next half hour, Jane asked question after question about Maura's experiences as a doctor and Starfleet officer. The captain was trying to get a feel of who Maura Isles was as not only an officer and doctor, but as a person as well.

"You are a very accomplished woman and I can see the dedication you have for your profession. You have the skills needed to fulfill the job as Chief Medical Officer, but I need to know how you are as a person."

Confused by the captain's question Maura asked, "What do you mean by as a person?"

Jane answered, "On a starship, the people who serve with you are not just your colleagues they are your family. Your family needs to know who you are, not just as the Chief Medical Officer and doctor. Tell me, who is Maura Isles?"

Looking at the woman before her Maura felt a sense belonging as she heard the woman's words. Yet, she was unable to answer the captain's question. How do you answer a question like that?

"I am unsure how to answer that question." Maura replied.

Although disappointed that she did not get an answer from the doctor, Jane was satisfied nonetheless.

"That's alright Dr. Isles; it is a very soul searching question and takes time to answer. But I do have an answer to the question you are about to ask.

Curious about the captain's words Maura asked, "How can you have an answer to a question that I have not asked?"

With a small smile Jane replied, "Ask me your question and I will give you an answer.

"What is your answer?" Maura asked.

A smile still adored Jane's lips as she stood and held her hand out to her new Chief Medical Officer, "Welcome aboard Dr. Isles. Welcome aboard."

* * *

Captain Rizzoli left her office about twenty minutes ago and Maura took the time to bask in her good fortunate. Maura let out a satisfied sigh as plopped herself down on long couch in her office.

The sound of silence was music to Maura's ears, but the silence broke before it even began.

Her combadge came to life, "I apologize for bothering you Dr. Isles, but you have an incoming communication from Garrett Fairfield."

Maura's eyes immediately popped open when she heard Garrett's name. She immediately sat up and tapped he combadge, "Thank you Holly, you can route it to my communication terminal."

"Understood," replied her assistant.

Getting off the couch and walking over to her desk she turned on her communication terminal. The screen came to life to show her former fiancé smiling at her.

Maura didn't return his smile; instead she gave him an angry and hurt look. "What do you want Garrett?" Maura asked angrily.

Garrett's smile did not waver, "I must have a reason to call my fiancée?"

"I'm your former fiancée. Last time I checked we haven't together in over two months," said an angry Maura.

The smile that Garrett was sporting disappeared as he shook his head, "How many times do I have to tell you? What happened between Carlota St. Pierce and me was a mistake."

Despite her strong objection to bad language Maura couldn't help the angry words that sprouted from her mouth, "You're damn right it was a mistake Garrett. I found you having sexual relations with Carlota St. Pierce in the home we shared together. Did you really think I was going to stay with you after that?"

"Are you really going to hold that against me? It's been two months Maura I haven't been with anyone else. I want to make this work again, please give me a chance to prove it to you." Garrett begged.

Maura knew exactly where this was going; she knew that when Garrett starts begging it means he gets what he wants. But not this time, this time Maura was ready.

"That won't work with me Garrett; I'm not going to allow you to hurt me again." Maura said, with confidence. "So why don't you leave me alone and let me move on with my life."

"Leave you alone and let you move on with your life." Garrett replied, with irritation. Her words caused Garrett's mind to go into overdrive. Then suddenly it hit him, "There's someone else isn't there? You're mine and mine alone."

Maura shook her head in disbelief. Not only will he not leave her alone, but he thinks he has the right to control her personal life. Wanting to rid herself of him Maura decided to give him the exact opposite of what he wanted.

"I am not your property Garrett; you have no right to say who I belong to." Maura said forcefully. "Now if you would excuse me Garrett I have more important duties to take care of."

"How dare you dare you speak to me that way! You would be nothing without me Maura. You and your family would still be at the short end of the stick if it wasn't for me and my family. You and your family would still be the laughing-stock of the social circle. Do you really want to go back to that?"

Maura shook her head in frustration. She despised the fact that the Fairfield's did help her and her family to become what they are today.

Garrett smiled smugly when he noticed the frustrated look on Maura's face. Seeing that he struck a chord in her he started to talk once again.

"Now that I have your attention Maura, how about going out with me tonight and we can reconsile of our engagement. What do you say to that, Maura?"

Something snapped with Maura when she heard Garrett's smug words. Deciding then and there that this was the last straw she spoke a calm, yet forceful tone.

"You listen to me and you better listen good. The answer is no Garrett; our engagement is over. So say goodbye Garrett."

Shocked and angry Garrett responded, "You will not refuse me Maura. I will tear you and your family down. I will-"

"You will what Garrett? My family is stable and I am prominent doctor and scientist among various societies. My family and I don't need to worry, but you on the other hand better watch yourself. I still am the only one that knows the truth of your infidelity during our engagement. I don't think the social circle will take kindly to such information."

"You wouldn't dare!" said the worried Fairfield.

Smirking a bit Maura replied, "I can and will if necessary Garrett. So if you want to keep that bit of information private then leave me alone."

Growling in frustration he snapped back at Maura, "I will hurt you Maura even if it is the last thing I do. What do you say to that?"

"Goodbye Garrett," responded Maura.

Without giving Garrett to speak she closed the communication link.

"Goodbye Garrett and hello new start."

* * *

**A/N: **I hope that the revamping of this chapter is much better than the original one for those that read the original one. Reviews are appreciated, but please be sure to keep them respectful.

**A/N #2: **Chapter Three will be taking longer to post since I am working with a beta reader and starting my senior year in college. **I urge readers read and review, but please don't send PMs to me about when I will have the next chapters up.**


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